System, device and methods of sample processing using semiconductor detection chips

ABSTRACT

Systems for processing a fluid sample to facilitate analysis with a semiconductor detection chip are provided herein. Such systems can include a sample processing cartridge coupleable with a chip carrier device configured for transport of the processed fluid sample from the sample cartridge. The chip carrier device can include one or more fluid channels extending between fluid-tight couplings attachable to transfer ports of the sample processing cartridge. The chip carrier device can include multiple portions or adapters, including a fluid sample portion, a flowcell portion and a chip carrier. Also provided are methods of preparing and transporting a fluid sample from a sample cartridge into a chip carrier device for analysis with a semiconductor detection chip carried within the chip carrier device.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.16/577,650, filed Sep. 20, 2019, which claims priority to U.S.Provisional Application No. 62/734,079 filed on Sep. 20, 2018, which isincorporated herein by reference in its entirety.

This application is generally related to PCT Application No. US2016/025748 entitled “Fluidic Bridge Device and Sample ProcessingMethods” filed April 2016; U.S. Pat. No. 6,374,684 entitled “FluidControl and Processing System,” filed Aug. 25, 2000; U.S. Pat. No.8,048,386 entitled “Fluid Processing and Control,” filed Feb. 25, 2002;and US 2017/0023281 entitled “Thermal Control Device and Methods of Use”filed Jul. 22, 2016; each of which is incorporated herein by referencein its entirety for all purposes.

BACKGROUND OF THE INVENTION

The present invention relates generally to fluid manipulation and, moreparticularly, to a device, system and method for processing a sample andfacilitating the transport of the prepared sample for further processingwith a semiconductor chip device, in particular a semiconductordetection chip.

In recent years, there has been considerable development in the use ofsemiconductor chips in performing fluid sample analysis (e.g. testing ofclinical, biological, or environmental samples). One continual challengehas been in performing processing of the fluid sample in preparation foranalysis with the semiconductor chips. Processing of such fluid samplestypically involves a series of processing steps, which can includechemical, optical, electrical, mechanical, thermal, or acousticalprocessing of the fluid samples. Whether incorporated into a bench-topinstrument, a portable analyzer, a disposable cartridge, or acombination thereof, such processing typically involves complex fluidicassemblies and processing algorithms. Developing a robust fluid sampleprocessing system can be extremely challenging and costly.

Conventional approaches for processing fluid samples typically involvessubstantial manual operation, while more recent approaches have soughtto automate many of the processing steps and can include the use ofsample cartridges that employ a series of regions or chambers eachconfigured for subjecting the fluid sample to a specific processingstep. As the fluid sample flows through the cartridge sequentially fromregion or chamber to a subsequent region or chamber of the cartridge,the fluid sample undergoes the processing steps according to a specificprotocol. Such systems, however, generally include an integrated meansof analysis, and are not typically amenable to use with a semiconductorchip. The standard approach of utilizing semiconductor detection chips,such as “lab on a chip” devices, generally requires a considerablycomplex, time-consuming and costly endeavor, requiring the chip beincorporated into a conventional chip package and then incorporated intomuch larger systems utilizing conventional fluidic transport means totransport a fluid sample to the chip device. The fluid sample istypically prepared by one or more entirely separate systems (oftenincluding manual interaction) and then pipetted into the fluid transportsystem to be supplied to the chip package. These challenges associatedwith pre and post testing processes often minimize the advantages andbenefits of such “lab on a chip” devices and present a practical barrierto their widespread use and acceptance in diagnostic testing.

Thus, there is a need for developing a device that performs a wide rangeof sample processing steps in a robust and consistent manner and that iscompatible for use with a semiconductor chip. There is further a needfor such methods and devices that allow for seamless integration withexisting technologies and to improve efficiency and throughput in fluidsample processing and handling and overcome the challenges describedabove.

BRIEF SUMMARY OF THE INVENTION

The present invention provides devices, methods and systems thatfacilitate processing of a fluid sample and transport of the processedsample for analysis with a semiconductor detection chip (also referredto as “chip”, “detection chip” or “semiconductor chip”). In one aspect,such methods and systems utilize existing sample processing technologiesto perform one or more processing steps, then transport the processedfluid sample to interface with a semiconductor chip and perform furtherprocessing with a semiconductor chip. Such further processing typicallyincludes analysis of a target analyte with a semiconductor detectionchip. In some embodiments, the invention further provides means for anyof: powering the chip, communicating, programming or signal processingwhen performing testing with a semiconductor detection chip.

In one aspect, the device is configured for use with any of a pluralityof differing types of chips and allows for a plug-n-play approach toutilizing semiconductor detection chips. For example, the device allowsthe system to be used as a platform to readily accept and utilizeexisting “lab on a chip” devices in a more cost effective manner. It isappreciated that the device can be configured for use with any type ofsemiconductor detection chip, including but not limited to CMOS,ion-sensitive FET (ISFET), bulk acoustic, non-bulk acoustic,piezo-acoustic, and pore array sensor chips. Further, the semiconductordetection chip can be adapted for use in an open package to any of themany JDEC standards, including but not limited to quad-flat no lead(QFN), dual in-line, and BGA array. Alternatively, the semiconductordetection chip can be mounted directly to the PCB as a chip-on-boardassembly. In some embodiments, the semiconductor detection chip servesas a biosensor that combines a biologically sensitive element with aphysical or chemical transducer to selectively (and in some embodiments,quantitatively) detect the presence of specific analytes in a fluidsample. In some embodiments, the chip provides an electrical or opticaloutput signal in response to a physical, chemical, or optical inputsignal. The device can further include features for powering,communication, signal integration, and data flow when performing testingwith the detection chip and can include software to facilitate use ofthe chip within the system. The device can further be configured tofacilitate testing with chip devices by utilizing various “on board”features, or can be configured for use with various “in board” or “offboard features”, as described in further detail below.

In one aspect, the invention pertains to a system for processing andanalyzing a fluid sample utilizing a sample cartridge and a chip carrierdevice coupled thereto. Such systems can include: a sample cartridgeconfigured to hold a biological sample, the sample cartridge comprisinga plurality of processing chambers fluidically interconnected by amoveable valve body; a module for performing sample preparation, themodule having a cartridge receiver adapted to receive and removablycouple with the sample cartridge; and a chip carrier device having afluidic interface configured for fluidically coupling with the samplecartridge. The fluidic interface is in fluid communication with aflowcell chamber of the device which is in fluid communication with asemiconductor detection chip when carried within the chip carrier of thedevice. The chip carrier device includes an electrical interfaceconfigured for powering the chip when supported within the carrier ofthe device. The electrical interface can further be configured tofacilitate communication with the chip, as well as signal processing andprograming.

In some embodiments, the chip carrier device can include variouschip-on-board features, such as any of those described herein. The chipcarrier device includes: a fluid sample adapter, a flowcell adapter, anda chip carrier components. The fluidic interface is configured forfluidically coupling with the sample cartridge, the fluidic interfacebeing in fluid communication with a first set of ports of the fluidsample adapter via a fluidic path. The flowcell adapter is coupleablewith the fluid sample adapter, the flowcell adapter defining theflowcell chamber in fluid communication with the fluid sample adapterwhen coupled thereto via one or more flowcell ports of the flowcelladapter. The chip carrier is coupleable with or integrated with theflowcell adapter and includes the carrier portion configured forsupporting a semiconductor chip. The chip carrier device can furtherinclude an electrical interface electrically connected to the carrierportion so as to power the chip when supported within the chip carrier.The chip carrier device can include various features “on board,”including any of a filter, pre-PCR chamber, a sonication chamber,valve/seats, thermocycling chamber, a magnetic separator, opticalinterrogation, opto-link, RF, magnetic or any feature or capabilitiesassociated with testing with chip devices.

In some embodiments, the device can be configured for use with various“in board” features of the system, for example, the chip carrier devicecan engage with an interface or separate device of the system configuredfor performing various functions, which may include but is not limitedto components for sample processing, thermal cycling, communication,testing, signal processing, etc. Such a system can include an electricalinterface or various other components that are separate from, butinterface with the chip carrier device.

In some embodiments, the chip carrier device is configured for use withvarious “off board” features, for example, the chip carrier device canfacilitate transport to an external device or interface or facilitatetransport of prepared fluid sample to a portion of a chip that isinterfaced with one or more external off-board components (e.g. thermalcycling, electro interface, detection interface). In some embodiments,the device can bridge or link to a standalone device or module, so as tofront-end a detection device, such as a MALDI-TOF, mass spectrometer,NMRI or other such detection device.

In some embodiments, the sample cartridge employs a rotary valveconfiguration to control fluidic movement within the cartridge thatallows for selective fluidic communication between a fluid sampleprocessing region and a plurality of chambers in the cartridge.Non-limiting exemplary chambers can include, a sample chamber, a reagentchamber, a waste chamber, a wash chamber, a lysate chamber, anamplification chamber, and a reaction chamber. The fluid flow among thefluid sample processing region and the chambers is controlled byadjusting the position of the rotary valve. In this way, the meteringand distribution of fluids in the cartridge can be varied depending onthe specific protocol, which allows sample preparation to be adaptableto different protocols such as may be associated with a particularsample type for different types of analysis or different types ofsamples. For example, the sample cartridge can include a means for celllysis, e.g., a sonication means so that bacteria and cells in a fluidsample to be analyzed can be lysed. Additional lysis means suitable foruse with the instant invention are well known to persons of skill in theart, and can include, chemical lysis, mechanical lysis, and thermallysis. In some embodiments, the sample includes bacteria, eukaryoticcells, prokaryotic cells, or viral particles.

In some embodiments, sample processing comprises sample processing stepsthat are performed from initial sample preparation steps, intermediateprocessing steps, and further processing steps to facilitate a detectionof a target analyte in the biological sample with the semiconductorchip. For example, sample processing can include preliminary preparationsteps, such as filtering, grinding, mincing, concentrating, trappingdebris or purifying a rough sample, or steps for fragmenting of DNA orRNA of the target analyte, such as by sonication or other mechanical orchemical means. Sample processing can include various intermediateprocessing steps, such as filtering, chromatography, or furtherprocessing of nucleic acids in the sample, including but not limited tochromatography, bisulfite treatment, reverse transcription,amplification, hybridization, ligation, or fragmentation of DNA or RNA.Sample processing may further include final processing steps, such asfinal amplification, hybridization, sequencing, chromatographicanalysis, filtering and mixing with reagents for a reaction to detectthe target analyte, which detection can include optical, chemical and/orelectrical detection. In some embodiments, the sample processing deviceis configured to perform initial and/or intermediate processing steps,while the semiconductor chip disposed within the device is configured toperform final processing, such as any of those described herein or aswould be known to one of skill in the art of target analyte detection.In some embodiments, the sample processing device is configured toperform at least a first step in the overall sample processing andtransport of the fluid sample to the semiconductor chip to perform atleast a subsequent step in the process, which can include detection ofthe target analyte. In another embodiment, the fluid sample can betransported from the semiconductor chip back to the sample processingdevice for additional processing. In some embodiments, to enableadditional new or enhanced functionality, one or more features thatprovide sample processing and/or sample preparation capabilitiesamenable to silicon-based technologies can be included on the siliconchip. For example, the chip could include one or more features for morerefined fluidic manipulation, further refined sample processing, or anycompatible sample processing and/or preparation steps. Such technologiesand functionalities could include but are not limited to:electrophoretic-based separation; fluidic pumping; andelectrowetting-based fluidic manipulation, including droplet generationor pumping, flow sensors, and the like. It is appreciated that thesechip features could be included in any of the embodiments describedherein, and further that the chip carrier can be adapted for use withsuch chip features.

In some embodiments, the sample processing device can be a fluid controland processing system for controlling fluid flow among a plurality ofchambers within a cartridge, the cartridge comprising a housingincluding a valve body having a fluid sample processing regioncontinuously coupled fluidically with a fluid displacement chamber. Thefluid displacement chamber is depressurizable to draw fluid into thefluid displacement chamber and pressurizable to expel fluid from thefluid displacement chamber. The fluid sample processing region includesa plurality of fluid transfer ports each fluidically coupled with one ofa plurality of external ports of the valve body. The fluid displacementchamber is fluidically coupled with at least one of the external ports.The valve body is adjustable with respect to the plurality of chamberswithin the housing to allow the external ports to be placed selectivelyin fluidic communication with the plurality of chambers. In someembodiments, the valve body is adjustable with respect to the housinghaving multiple chambers, to place one external port at a time influidic communication with one of the chambers.

In some embodiments of the cartridge, the fluid sample processing regioncan be disposed between the fluid displacement chamber and at least onefluid transfer port. The term “fluid processing region” refers to aregion in which a fluid sample is subject to processing including,without limitation, chemical, optical, electrical, mechanical, thermal,or acoustical processing. For example, chemical processing may include achemical treatment, a change in pH, or an enzymatic treatment; opticalprocessing may include exposure to UV or IR light; electrical processingmay include electroporation, electrophoresis, or isoelectric focusing;mechanical processing may include mixing, filtering, pressurization,grinding or cell disruption; thermal processing may include heating orcooling from ambient temperature; and acoustical processing may includethe use of ultrasound (e.g. ultrasonic lysis). In some embodiments, thefluid processing region may include an active member, such as a filter,to facilitate processing of the fluid. Non-limiting exemplary activemembers that are suitable for use with the instant invention include amicrofluidic chip, a solid phase material, a filter or a filter stack,an affinity matrix, a magnetic separation matrix, a size exclusioncolumn, a capillary tube, or the like. Suitable solid phase materialsinclude, without limitation, beads, fibers, membranes, filter paper,lysis paper impregnated with a lysing agent, glass wool, polymers, orgels. In some embodiments, the fluid processing region is used toprepare a sample for further processing, for instance, in asemiconductor chip device fluidly coupled with the fluid sampleprocessing device. Additional active members suitable for use with theinstant invention are well known to persons of skill in the art. In someembodiments, an energy transmitting member is operatively coupled withthe fluid sample processing region for transmitting energy thereto toprocess fluid contained therein. In some embodiments, the valve bodyincludes a crossover channel, and the valve body is adjustable withrespect to the plurality of chambers to place the crossover channel influidic communication with two of the chambers concurrently. Thecartridge housing includes one or more branches that extend to one ormore transfer ports to which a reaction vessel can be attached so as tofacilitate transfer of fluid sample from a chamber of the cartridge intothe reaction vessel. In some embodiments, the reaction vessel extendsfrom the housing of the cartridge. These aspects can be understoodfurther by referring to U.S. Pat. No. 8,048,386. It is understood thatfluid may flow in either direction into or out of the transfer ports invarious embodiments fluid flow is not limited in any particulardirection. For example, in an embodiment having a pair of transferports, air may be pumped into or evacuated from one of the pair oftransfer ports to facilitate flow of the fluid sample into a conduit ofthe reaction vessel through the fluid transfer port.

In some embodiments, chip carrier device includes fluid sample adapterhaving a pair of fluid channels have a cross-sectional lumen area thatdoes not substantially vary from each other. The cross-sectional area ofeach of the fluid channels remains a substantially constant size andshape between respective fluid-tight couplings. In some embodiments, thepair of fluid channels are spaced apart and dimensioned so as to befittingly received within two corresponding transfer ports in a samplecartridge housing. In some embodiments, the fluid sample adapter caninclude a supporting web structure separating the at least two channels.In some embodiments, the fluid sample adapter can be configured so thatthe volume of each of the at least two channels, does not substantiallydiffer, while in other embodiments, the channels are configured to havesubstantially different volumes.

In some embodiments, the one or more fluid channels of the fluid sampleadapter include a chamber configured for initial sample preparationsteps, such as initial filtering of debris from the fluid sample,initial mixing with reagents, and/or initial fragmentation of the DNA ofthe target analyte, such as a sonication chamber or sharp edges adaptedfor adapted for breaking or fragmenting cells or DNA strands. In someembodiments, the one or more fluid channels include one or more regionsthat can be adapted for providing controlled flow of the fluid sample,such as may be used for transitive storage or collection of the fluidsample. Such regions can also be used for example in mixing,pre-amplification, or to facilitate preparation or analysis of the fluidsample.

In some embodiments, the fluid sample adapter includes fluid-tightcouplings, each defined as a stub dimensioned to be fittingly receivedwithin one or more corresponding ports in the sample cartridge. Thestubs can be dimensioned to be fluidly coupled by a friction fit withinthe corresponding ports in the sample cartridge or a cartridge housingthat is inserted into the sample cartridge. In some embodiments, thefluid sample adapter includes a pair of fluid channels fed by two inletstubs that are fittingly received along a portion of the cartridgehousing having two fluid transfer ports. In some embodiments, the fluidtight couplings can include a leur-lock connection, a friction fitconnection, a screw type connection, a click-fit connection, and thelike.

In some embodiments, the fluid sample adapter includes a flange fromwhich the inlet stubs extend, the flange being engageable with aretaining member of the sample cartridge so as to maintain the fluidtight coupling and position of the chip carrier device when coupled tothe sample cartridge. The sample cartridge can also include a gasketsurrounding the plurality of fluid transfer ports, the gasket being of aformable material, such as an elastomeric material, so that when theinlet portions of the first end of the chip carrier device are fluidlycoupled with the at least two fluid transfer ports, the gasket memberengages a proximal facing surface of the flange so as to ensure afluid-tight coupling.

In some embodiments, the chip carrier device can include one or morefeatures for further processing of the fluid sample during transportthrough the chip carrier device. In some embodiments, the chip carrierdevice can include at least one processing region in fluid communicationwith at least one of the fluid channels, wherein the processing regionis not a sample preparation chamber. In some embodiments, the chipcarrier device includes a pre-amplification chamber and/or anamplification chamber for carrying out a polymerase chain reaction orother suitable nucleic acid amplification test (NAAT). In someembodiments, the chip carrier device includes a flowcell adapted tointerface with an active area of the semiconductor chip carried withinthe chip carrier device. In one aspect, the flowcell adapter facilitatesdirect contact of the fluid sample with the active area of the chip. Insome embodiments, at least a portion of the chip carrier device is atleast partly translucent or transparent so as to allow confirmation thatthe fluid sample is passing through the fluid sample adapter by visualobservation or optical monitoring. In some embodiments, the fluid sampleadapter can include one or more features that may provide an additionalprocess step, for example, a chamber for chemical treatment, such asbisulfite treatment, a pre-amplification chamber or filter, or featuresthat facilitate passage of the fluid sample through the fluid sampleadapter, such as a gas permeable vent or a bubble trap.

In some embodiments, the chip carrier device is of sufficient length anddimension that when coupled with a sample cartridge mounted within acartridge receiver of a sample cartridge processing module having apassageway, the carrier extends to an instrument interface including anarray of electrode contacts that connect with corresponding electrodecontacts of an electrical interface board of the chip carrier device tofacilitate operation of the semiconductor chip through the instrumentinterface.

In some embodiments, the chip carrier device is defined by one or morecomponents formed of a planar frame supporting and defining one or morefluidic channels. Each of the planar frames can be formed of asufficiently stiff material, typically a polymer-based material, so asto support the one or more fluidic channels so that the chip carrierdevice extends laterally from the sample cartridge to interface with theinstrument interface. In some embodiments, the one or more planar framesare sufficiently rigid so as to withstand a normal force against theplanar frames from the electrical contacts of the instrument interfacewhen engaged against the electrical interface board of the chip carrierdevice. Typically, the electrical contacts of the instrument interfaceare pogo pins that resiliently engage the electrical contact pads of theinterface of the chip carrier device when the instrument interface boardis engaged against the chip carrier device. In some embodiments, theinstrument interface board is configured so as to move or pivot towardthe chip carrier device so as to securely engage correspondingelectrical contacts when a sample cartridge coupled with a chip carrierdevice is received within the module. In other embodiments, theelectrical contacts could be configured as an edge connector. It isappreciated that the electrical contacts could be configured to connectby any suitable means or to accommodate any connection standard orarrangement.

Another aspect of the invention provides for methods of processing andanalyzing a sample utilizing a chip carrier device as provided herein.Such methods can include steps of: receiving a sample cartridge at acartridge receiver of a module, the sample cartridge comprising aplurality of processing chambers fluidically interconnected by a one ormore mechanisms; receiving an electronic instruction to process theunprepared sample into a prepared sample from a processing control unitof the cartridge receiver; performing a sample preparation method toprocess the unprepared sample into the prepared sample; and fluidicallymoving the prepared sample into a chip carrier device fluidly coupledwith the sample cartridge. Such methods can further include performingan analysis of the fluid sample using an active element of a chipsupported within the chip carrier device via processing control unit ofthe cartridge processing module electrically coupled with the chipthrough an instrument interface of the module.

Another aspect of the invention provides for methods of transporting afluid sample between a sample processing device, such as the samplecartridge, and a semiconductor chip as provided herein. A non-limitingexemplary method includes fluidly coupling a sample processing devicewith a semiconductor chip via a chip carrier device carrying thesemiconductor chip, the chip carrier device being fluidically coupledwith the sample cartridge via one or more fluid ports. In someembodiments, the chip carrier device is configured to utilize one ormore fluid ports on a sample processing device (e.g., a samplecartridge) to allow for sample processing in a sample processing device(e.g., sample preparation) before transport of the processed fluidsample into the chip carrier device via the one or more fluid ports forsubsequent processing (e.g., analysis) with a semiconductor chip of thecarrier. In some embodiments, the method further includes controllingthe semiconductor chip with an instrument interface of the module inwhich the sample cartridge is received. In some embodiments, the methodfurther includes controlling the chip in the carrier with a controlmodule that is separate from the module, for example, part of an add-onmodule that interfaces with the semiconductor chip from outside themodule or through an access passageway of the module. In someembodiments, fluid flow through the one or more channels can be effectedthrough pressurization/depressurization or by displacement of the fluidsample by the sample processing devices. Typically, an instruction fortransport of the fluid sample from the cartridge into the chip carrierdevice is provided by a control unit of the module that receives thesample cartridge and controls sample preparation therein. It isappreciated that various alternative configurations may be used inproviding motive force for transfer of the fluid sample through the chipcarrier device with the module through the fluid sample cartridge.

In some embodiments, methods for processing an unprepared sample caninclude steps of: receiving a sample cartridge in a cartridge receiverof a module, the sample cartridge including a biological fluid sample tobe analyzed, a plurality of processing chambers fluidicallyinterconnected by a moveable valve body; receiving an electronicinstruction to process the biological sample into a prepared sample fromthe module; performing a sample preparation method in the samplecartridge to process the biological fluid sample into the preparedsample; transporting the prepared sample into a chip carrier devicefluidically coupled with the sample cartridge; and performing analysisof the biological fluid sample with a chip carried within the chipcarrier device. In some embodiments, transporting the sample may includesteps of: moving a cartridge interface unit to move the valve body tochange fluidic interconnections between the plurality of sampleprocessing chambers; applying pressure to a pressure interface unit tomove fluid between the plurality of processing chambers according toposition of the valve body; and fluidically moving the prepared sampleinto the chip carrier device. Performing analysis of the fluid samplecan include controlling operation of the chip with the module via aninstrument interface board electrically coupled with an electricalinterface board of the chip carrier device. Any result of the analysiscan be obtained by the module via the electrical interface andcommunicated to various other devices as desired.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an overview of a sample cartridge fluidically coupled with achip carrier device and an associated instrument interface board of amodule for receiving and operating the sample cartridge in accordancewith some embodiments of the invention.

FIG. 2A illustrates the instrument interface board of the module, theinstrument interface board having an array of electrical contacts forinterfacing with electrical contact pads of the chip carrier device whenthe sample cartridge is received within the module, as shown in FIG. 2B,in accordance with some embodiments.

FIG. 3 illustrates a detailed view of the sample cartridge fluidicallycoupled with a chip carrier device, in accordance with some embodiments.

FIGS. 4A-4C illustrate various views of a fluid sample adapter componentof the chip carrier device, in accordance with some embodiments.

FIGS. 5A-5C illustrate various views of a chip carrier component of thechip carrier device, in accordance with some embodiments.

FIGS. 6A and 6B illustrate a detailed view and a cross-sectional view ofan assembled chip carrier device, in accordance with some embodiments.

FIGS. 7A and 7B illustrate detailed views of an assembled chip carrierdevice, in accordance with some embodiments.

FIGS. 8 and 9 illustrate the fluid sample adapter component and anassembled chip carrier device, respectively, coupled with a samplecartridge, in accordance with some embodiments.

FIG. 10 illustrates an alternative chip carrier device coupled to asample cartridge, the device including a fluid sample adapter, flowcelladapter and chip carrier component, in accordance with some embodiments.

FIGS. 11A-11C illustrate various views of a fluid sample adaptercomponent of a chip carrier device, in accordance with some embodiments.

FIGS. 12A-12C illustrate various views of a flowcell adapter componentof a chip carrier device, in accordance with some embodiments.

FIGS. 13A-13C illustrate various views of a chip carrier component of achip carrier device, in accordance with some embodiments.

FIGS. 14A-14B illustrate a chip carrier component coupled with aflowcell adapter component, in accordance with some embodiments.

FIGS. 15A-15C illustrate various views of an assembled chip carrierdevice, in accordance with some embodiments.

FIG. 16 illustrates a sample cartridge coupled with a fluid sampleadapter component of a chip carrier device and FIG. 17 illustrates anassembled chip carrier device coupled with the sample cartridge, inaccordance with some embodiments.

FIG. 18 illustrates alternative embodiments employing differentdetection modes, each configured for use with a sample cartridge, inaccordance with some embodiments.

FIGS. 19-20 illustrate methods of processing a sample with asemiconductor chip utilizing sample processing in a sample cartridge, inaccordance with some embodiments.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates generally to a system, device and methodsfor fluid sample manipulation and analysis, in particular, for transportof a fluid sample from a sample processing device into a chip carrierdevice for analysis using a semiconductor chip.

I. Exemplary System Overview

In one aspect, the invention relates to a chip carrier device having oneor more fluid conduits that are fluidly coupleable with one or moreports of a sample cartridge to facilitate transport of a processed fluidsample from the cartridge into the chip carrier device through the oneor more fluid conduits for further processing with a semiconductor chipin the chip carrier device. In some embodiments, the sample cartridge isreceived by a module which facilitates operation of the sample cartridgeto perform processing and transport of the processed fluid sample intothe chip carrier device and further includes an instrument interfacethat electrically connects to the chip carrier device to facilitateoperation of the semiconductor chip carried within the device.

In some embodiments, the chip carrier device can include a variety offeatures, such as one or more specific regions, each region adapted fora sample processing procedure or a sample analysis procedure.Non-limiting exemplary sample processing procedures can include,filtration, concentration, incubation, mechanical, electrical, optical,chemical treatment and/or amplification. In some embodiments, the chipcarrier device includes a pre-amplification region for conducting apolymerase chain reaction or other type of nucleic acid amplificationprocedure as known to persons of skill in the art. Additional sampleprocessing procedures suitable for use with the invention are well knownto persons of skill in the art. Non-limiting exemplary sample analysisprocedures can include, amplification, hybridization, opticalinterrogation, iso-electric focusing, antibody binding and detection(e.g. ELISA), sequencing, chromatography, and lateral flowchromatography. Additional sample analysis procedures suitable for usewith the invention are well known to persons of skill in the art. Thechip carrier device can further include one or more features, includingfilters, traps, membranes, ports and windows, to allow additionalprocessing steps during transport of the fluid sample to thesemiconductor chip.

A. Sample Cartridge Device

The sample cartridge device can be any device configured to perform oneor more process steps relating to preparation and/or analysis of abiological fluid sample according to any of the methods describedherein. In some embodiments, the sample cartridge device is configuredto perform at least sample preparation. The sample cartridge can furtherbe configured to perform additional processes, such as detection of atarget nucleic acid in a nucleic acid amplification test (NAAT), e.g.,Polymerase Chain Reaction (PCR) assay, by use of a reaction tubeattached to the sample cartridge. Preparation of a fluid samplegenerally involves a series of processing steps, which can includechemical, electrical, mechanical, thermal, optical or acousticalprocessing steps according to a specific protocol. Such steps can beused to perform various sample preparation functions, such as cellcapture, cell lysis, binding of analyte, and binding of unwantedmaterial.

A sample cartridge suitable for use with the invention, includes one ormore transfer ports through which the prepared fluid sample can betransported into a reaction tube for analysis. FIG. 1 illustrates anexemplary sample cartridge 100 suitable for use with a chip carrierdevice in accordance with some embodiments. Conventionally, such asample cartridge is associated with a reaction tube 110 (see embodiment0 in FIG. 18 ) adapted for analysis of a fluid sample processed withinthe sample cartridge 100. Such a sample cartridge 100 includes variouscomponents including a main housing having one or more chambers forprocessing of the fluid sample, which typically include samplepreparation before analysis. In accordance with its conventional use,after the sample cartridge 100 and reaction tube 110 are assembled (asshown in FIG. 18 ), a biological fluid sample is deposited within achamber of the sample cartridge and the cartridge is inserted into acartridge processing module configured for sample preparation andanalysis. The cartridge processing module then facilitates theprocessing steps needed to perform sample preparation and the preparedsample is transported through one of a pair of transfer ports into fluidconduit of the reaction tube 110 attached to the housing of the samplecartridge 100. The prepared biological fluid sample is then transportedinto a chamber of the reaction tube 110 where the biological fluidsample can undergo nucleic acid amplification. In some embodiments, theamplification is a polymerase chain reaction. In some embodiments,concurrent with the amplification of the biological fluid sample, anexcitation means and an optical detection means of the module is used todetect optical emissions that indicate the presence or absence of atarget nucleic acid analyte of interest, e.g., a bacteria, a virus, apathogen, a toxin, or other target analyte. It is appreciated that sucha reaction tube could include various differing chambers, conduits, ormicro-well arrays for use in detecting the target analyte. The samplecartridge can be provided with means to perform preparation of thebiological fluid sample before transport into the chip carrier device.Any chemical reagent required for viral or cell lysis, or means forbinding an analyte of interest (e.g. reagent beads) can be containedwithin one or more chambers of the sample cartridge, and as such can beused for sample preparation.

An exemplary use of a reaction tube for analyzing a biological fluidsample is described in commonly assigned U.S. Pat. No. 6,818,185,entitled “Cartridge for Conducting a Chemical Reaction,” filed May 30,2000, the entire contents of which are incorporated herein by referencefor all purposes. Examples of the sample cartridge and associated moduleare shown and described in U.S. Pat. No. 6,374,684, entitled “FluidControl and Processing System” filed Aug. 25, 2000, and U.S. Pat. No.8,048,386, entitled “Fluid Processing and Control,” filed Feb. 25, 2002,the entire contents of which are included as an appendix, and areincorporated herein by reference in their entirety for all purposes.

Various aspects of the sample cartridge 100 shown in FIGS. 3-17 can befurther understood by referring to U.S. Pat. No. 6,374,684, whichdescribed certain aspects of a sample cartridge in greater detail. Suchsample cartridges can include a fluid control mechanism, such as arotary fluid control valve, that is connected to the chambers of thesample cartridge. Rotation of the rotary fluid control valve permitsfluidic communication between chambers and the valve so as to controlflow of a biological fluid sample deposited in the cartridge intodifferent chambers in which various reagents can be provided accordingto a particular protocol as needed to prepare the biological fluidsample for analysis. To operate the rotary valve, the cartridgeprocessing module comprises a motor such as a stepper motor that istypically coupled to a drive train that engages with a feature of thevalve in the sample cartridge to control movement of the valve andresulting movement of the fluid sample according to the desired samplepreparation protocol. The fluid metering and distribution function ofthe rotary valve according to a particular sample preparation protocolis demonstrated in U.S. Pat. No. 6,374,684, which is incorporated hereinfor all purposes.

It is appreciated that the sample processing cartridge described aboveis but one example of a sample processing device suitable for use with achip carrier device in accordance with embodiments as described herein.While chip carrier configurations that allow for use of such a sampleprocessing cartridge are particularly advantageous as they allowutilization of conventional fluid sample cartridges, it is appreciatedthat the concepts described herein are applicable to various othersample processing devices, which can include various other samplecartridge configurations or other fluid sample processing devices andcomponents.

B. Chip Carrier Device

The chip carrier device is adapted to fluidically couple a semiconductorchip to a sample cartridge as described herein. In some embodiments, thechip carrier device includes an electrical interface adapted tointerface with an instrument interface board of a sample processingmodule which operates the sample processing cartridge. It is appreciatedthat the chip carrier device can be configured for use with any type ofchip, including but not limited to CMOS, ISFET, bulk acoustic, non-bulkacoustic, piezo-acoustic, and pore array sensor chips. Further, the chipcan be adapted for use in an open package to any of the many JDECstandards, including but not limited to QFN, dual in-line, and BGAarray. Alternatively, the chip can be mounted directly to the PCB as achip-on-board assembly. In some embodiments, the chip carrier device isdesigned to allow analysis of the biological fluid sample with the chipby electrical operation of the chip by the instrument interface of themodule. This is accomplished through electrical contact pads of the chipcarrier device that are electrically connected to the chip and whichinterface with the instrument interface of the module.

A configuration as described above allows for a more seamless transitionbetween processing of the fluid sample with the sample cartridge andsubsequent processing or analysis of the fluid sample with the chip inthe chip carrier device. This configuration facilitates industrydevelopment of semiconductor chip devices by standardizing processing orpreparation of the sample and delivery of the processed sample to thechip device. Preparation of the sample can be a time consuming andlaborious process to perform by hand and can be challenging to developwithin a next generation chip device. By utilizing a chip carrier deviceinstead of the reaction tube, the user can utilize the sample cartridgeto prepare the sample in a sample cartridge and subsequently transportthe prepared sample into the attached chip carrier device for analysiswith the semiconductor chip carried therein. Such a configurationexpedites development of semiconductor chip by utilizing existing samplepreparation processes, configured for PCR detection, and allowing use ofsuch processes with a semiconductor chip device.

In some embodiments, the chip carrier device can include one or moreprocessing features in fluid communication with one or more of the fluidflow channels, such as one or more chambers, filters, traps, membranes,ports and windows, to allow additional processing steps during transportof the fluid sample to the second sample processing device. Suchchambers can be configured for use with an amplification chamber toperform nucleic acid amplification, filtration, chromatography,hybridization, incubation, chemical treatment, e.g., bisulfite treatmentand the like. In some embodiments, the chamber allows for accumulationof a substantial portion of the fluid sample, if not the entire fluidsample, for further processing or analysis as needed for a particularprotocol. In some embodiments, the chamber comprises a window that is atleast partly transparent, which allows for optical detection of ananalyte of interest in the fluid sample through the chamber duringtransport of the fluid sample through the chip carrier device. Thisfeature is particularly advantageous when screening for the presence orabsence of multiple analytes, or for an analysis that may requireseveral or redundant detection steps or require further processingand/or analysis of the fluid sample after detection of a particulartarget or analyte of interest.

C. Instrument Interface

The instrument interface of the module is a circuit board adapted toengage an electrical interface of the chip carrier device to allow themodule to electrically control the semiconductor chip. In someembodiments, the instrument interface is located within a common housingof the module to provide more seamless processing between the fluidsample cartridge and the chip carrier device. The instrument interfacecan be controlled by the module in coordination with transport of thefluid sample from the sample cartridge to the semiconductor chip.

In some embodiments, instrument interface board is mechanically mountedon a pivot that moves toward the chip carrier device when receivedwithin the module. The instrument interface board is configured to pivotfrom an open position before the sample cartridge is loaded to anengaged position when loaded. A cam (not shown) positions the interfaceboard into contact with the electrical interface board on the chipcarrier device. Pogo pins on the instrument interface board contact theelectrical contact pads on the electrical interface board to allow themodule to control analysis of the fluid sample with the chip carriedwithin the chip carrier device.

In some embodiments, the chip carrier device is configured with fluidflow channels of similar flow dimensions as the fluid channels with thereaction tube 110 noted above (see U.S. Pat. No. 6,374,684). This allowsthe same mechanisms by which fluid sample is transported through thereaction tube to be used to transport fluid sample into the chip carrierdevice. A person of skill in the art would appreciate that transport ofthe fluid sample into the chip carrier device can be effected in anynumber of ways in accordance with various other aspects of the inventiondescribed herein.

II. Example Chip Carrier Devices and Associated Systems A. SystemOverview

FIG. 1 illustrates an overview of a system utilizing a conventionalfluid sample cartridge 100 fluidically coupled with a chip carrierdevice 200. The fluid sample cartridge 100 is adapted for insertion intoa bay of a processing module configured to perform one or moreprocessing steps on a fluid sample contained within the fluid samplecartridge through manipulation of the fluid sample cartridge. Aninstrument interface 300 of the module is incorporated into the modulewithin the bay in which cartridge 100 is received and includes a plate301 having a receptacle opening 302 through which the chip carrierdevice 200 extends when cartridge 100 is positioned within the bay. Theinstrument interface 300 further includes an instrument board 310, suchas a PCB board, that extends alongside a major planar surface of chipcarrier device 200 and includes electrical contacts 312 arranged so asto electrically couple with corresponding contact pads on the majorplanar surface of the chip carrier device.

FIG. 2A illustrates the instrument interface board 310 of the module andthe electrical contacts 312 for interfacing with electrical contact padsof the chip carrier device. Typically, the contacts 312 are arranged ina pattern, such as a rectangular array, that corresponds to the contactsof the chip carrier device. In one aspect, the electrical contacts areconfigured to facilitate on-board electrical connections. In thisembodiment, the contacts 312 are configured as pogo-pins so as todeflect upon insertion of the chip carrier device 200 through receptacleopening 302 to provide secure electrical coupling between contacts 312and corresponding contacts on chip carrier 230 of the chip carrierdevice 200, as shown in FIG. 2B. Although a rectangular array ofpogo-pins is depicted here, it is appreciated that the electricalcontacts could be arranged in various other patterns, in accordance witha corresponding chip carrier device and that various other contactconstructions could be realized. In some embodiments, the electricalcontacts could be configured as one or more edge connectors or othertypes of multi-pin connector arrangements. It is further appreciatedthat the instrument interface need not utilize every contact so as to becompatible for use with a carrier having differing numbers orarrangements of contact pads, as desired. In some embodiments, theelectrical contacts could include an additional adapter so as to besuitable for use with various differing types of chip carrier devices.In some embodiments, it may be cost effective to package a semiconductorcontroller as an adjunct to the chip carrier such that the signalconnectivity is minimized. Such an approach could use any suitableconnector means, which can include a standard connector type, such as aUSB interface (e.g. [+1, −2, sig 3, sig 4]).

A. Fluid Sample Adapter

FIG. 3 illustrates a detailed view of the sample cartridge 100fluidically coupled with chip carrier device 200, in accordance withsome embodiments. In this embodiment, the chip carrier device 200includes a fluid sample adapter 201 having a fluid flow portion on oneside and a flowcell portion on the opposing side. As can be understoodfurther by referring to FIGS. 4A-4B, the fluid sample adapter 201fluidically couples to the sample cartridge 100 by a fluidic interface211 having a pair of fluid ports 212, 214 that couple with correspondingfluid ports of the sample cartridge. On one side, the fluid sampleadapter 201 includes a fluid flow portion 210 defined therein, as shownin FIG. 4A, while on the opposing side, the fluid sample adapter has aflowcell portion 220 defined therein, as shown in FIG. 4B. The flowcellportion 220 is fluidically coupled with the fluid flow portion 210 suchthat fluid introduced through a fluid inlet of the fluidic interface 211flows through the fluid flow portion 210 before flowing into a flowcell224 defined in the flowcell portion 220. The flowcell portion 220 isconfigured to couple with a chip carrier portion 230 such that a chipcarried within the chip carrier portion 230 engages against the flowcellchamber 224. The flowcell portion 220 can include one or more couplingfeatures 229 (e.g. six protruding knobs about the perimeter of a majorface) to facilitate alignment and secure coupling of the chip carrierportion 230 with the fluid sample adapter 201. Any or all of the adapteror flow cell portion of the chip carrier device are formed from asuitably rigid material such that the chip carrier device 200 extendsoutward from the sample cartridge 100. In some embodiments, the chipcarrier device 200 is supported only by a pair of inlet stubs of thefluidic interface of the fluid sample adapter 201 fittingly receivedwithin the corresponding pair of fluid ports of sample cartridge 100 anda surrounding flange.

B. Fluid Flow Portion

FIGS. 4A-4C depict an exemplary fluid sample adapter device inaccordance with some embodiments. As shown in FIG. 4A, the fluid sampleadapter portion 210 includes two fluid channels or conduits spaced apartand extending within the chip carrier device. The channels are separatedand supported by a supporting web structure. The chip carrier device canbe fabricated from any material suitable for transport of a fluid sampleselected so as to not interfere with processing or analysis of thesample, typically an inert plastic or polymer-based material can beused. In some embodiments, the components of the chip carrier are formedof polycarbonate, polysulfone, or any suitable material (e.g. anymaterial compatible with an adhesive). In some embodiments, the materialis compatible with a silicone adhesive. In some embodiments, thematerial used to fabricate the chip carrier device is a transparent orpartly translucent material to allow visual observation of sampletransport and/or optical detection/monitoring of the fluidic channelthrough the material.

In some embodiments, the chip carrier device includes a fluid sampleadapter configured with the same Luer ports and flange arrangement ofthe fluidic interface as a typical PCR reaction tube so that the fluidsample adapter can easily interface with sample cartridges. The fluidsample adapter is configured such that the ports connect fluidically toan optional PCR pre-amplification chamber. Alternatively, theamplification chamber could house a filter, an affinity matrix, amagnetic capture zone, or other active area that can be manipulated bythe module. Typically, the fluidic pathways are defined in a firstsubstrate and sealed by a second substrate, such as a thin film, similarto the construction of conventional PCR reaction tubes. In someembodiments, the fluid sample adapter also features alignment andassembly bosses as well as mechanical snaps so that a chip carriercomponent or chip can be secured against a flowcell of the flowcellportion with ease.

In some embodiments, the length of the fluid sample adapter is about 12cm, 11 cm, 10 cm, 9 cm, 8 cm, 7 cm, 6 cm, 5 cm, 4 cm, 3 cm, 2 cm, or 1cm in length. In some embodiments, the fluid sample adapter 210 has alength between 3 to 5 cm, such as about 4 cm from the flange of thefluidic interface 211, and the fluid channels extend in parallel and areseparated by about 1 cm. This configuration allows for substantiallyfluid-tight couplings that are of substantially the same construction asa conventional reaction tube. The fluid-tight couplings of each channelare defined by a stub, each stub being dimensioned to be fittinglyreceived in a corresponding external port of the sample cartridge tofacilitate a fluid-tight coupling of the fluid channels withcorresponding fluid channels of the chip carrier device. For example,stubs along fluid inlets and outlet 212, 214 at the fluidic interface211 at the proximal end of the chip carrier device 200 serve as inletstubs for flow of the prepared fluid sample into through the fluidicpath of the fluid flow portion 210. In some embodiments, these stubs canhave an outside diameter between 2-10 mm, for example, the outsidediameter can be 2, 3, 4, 5, 6, 7, 8, 9, or 10 mm. Typically, the outsidediameter of the stub is about 3 mm, and extends from the flange adistance of about 2-5 mm, such as about 3 mm, to facilitate fluid-tightcoupling. In some embodiments, the inside diameter of each of the one ormore channels within any of the components of the chip carrier devicecan be within a range of 1 mm to 5 mm.

In some embodiments, the fluid sample adapter 201 includes one or morechannels that extend between fluid-tight couplings without any chambers,valves or ports between the proximal and distal ends. In someembodiments, the fluid sample adapter 201 includes one or more valves,or ports. In some embodiments, the one or more channels can include oneor more chambers or regions, which can be used to process or analyze thefluidic sample. For example, the fluid sample adapter can include one ormore chambers or regions for thermal amplification of a nucleic acidtarget in the sample, filtration of the sample, chromatographicseparation of the sample, hybridization, and/or incubation of the samplewith one or more assay reagents.

While the fluid tight couplings shown in FIG. 4A includes stubsextending from a flange of the fluidic interface 210, it is appreciatedthat various other fluid-tight couplings suitable for use with theinvention can be devised as needed to fluidly couple with other types ofdevices. Non-limiting exemplary fluid type couplings suitable for usewith the invention, include, Luer-lock connections, snap-fitconnections, friction fittings, click-fit connections, and screw-onconnections. Additional types of fluid tight couplings suitable for usewith the invention are well known to persons of skill in the art.

As can be seen in FIGS. 4A-4C, the fluid sample adapter 201 is definedby one or more planar substrates defining a fluidic path 213 coupled toa fluidic interface 211. The fluidic interface 211 is a structuralmember from which a majority of the planar frame cantilevers when thefluidic interface 211 is coupled with the sample cartridge. The fluidicinterface 211 can be integrally formed with the planar frame. Thefluidic interface 211 also serves as a mechanical coupling to samplecartridge 100. Fluidic interface 211 includes a fluidic inlet 212 andfluidic outlet 214, which provides a fluidic interface to the samplecartridge device. Each of the fluidic inlet 212 and fluidic outlet 214are fluidically coupled to fluidic path 213 that is formed in the planarsubstrate. It is appreciated that the fluid sample adapter 210 and thefluidic interface 211 can be integrally formed as a single component.

In some embodiments, the fluidic path 213 is defined primarily along onemajor face of the planar substrate and enclose by a second planarsubstrate, for example, a thin film heat sealed on the substrate so asto enclose the channels and chambers defined within the substrate. Thefluidic path 213 leads to a flowcell interface that extends width-wisethrough the fluid sample adapter 201 into a set of flowcell ports 226,228 of a flowcell 224 defined in the flowcell adapter portion 220defined on the opposite side of the fluid sample adapter 201. In thisembodiment, the flowcell interface includes an inlet flowcell port 228and outlet flowcell port 226, which allow for controlled fluid transportthrough the fluid sample adapter 201 into the flowcell chamber 224 viathe fluidic inlet 212 and fluidic outlet 214. Typically, the flowcellinlet 228 is disposed below the flowcell outlet 226 when the fluidsample adapter 201 is oriented vertically to facilitate controlled fluidflow through the flowcell chamber 224. In this embodiment, the fluidicchannels are defined along one major face of the fluid sample adapter201 and the flowcell portion is defined within the opposing major face.In this embodiment, these portions are formed as an integrally formedcomponent. It is appreciated, however, that the fluidic sample adaptercan be formed from one or more components.

It should be understood that use of the terms “inlet” and “outlet” donot limit function of any fluid inlets or outlets described herein.Fluid can be introduced and evacuated from both or either. In someembodiments, the fluidic path 213 is valveless, and thus externalincreases or decreases in pressures can be applied via the fluidic inlet212 and fluidic outlet 214 by an external system to move fluid withinthe fluidic path 213, which extends from the fluidic inlet 212 to thefluidic outlet 214. The cross-section of the fluidic path 213 can beround or rectangular, and can have diameters or widths ranging fromabout 50 m to about 2 mm. Typically, the diameters or widths range fromabout 250 m to about 1 mm. In this embodiment, the fluidic path 213includes a chamber 215, which is an enlarged portion of fluidic path 213between the flowcell 224 and the fluidic inlet 212, the chamber beingdimensioned to contain a substantial portion or an entirety of a fluidsample transported from the sample cartridge to facilitate variousprocesses, including but not limited to flow metering, mixing,pre-amplification, thermal cycling, or any other sample processingdesired. It is appreciated that various other components could beincorporated into fluid sample adapter, for example, a valve, filter,window, or any other feature desired.

In some embodiments, the chip carrier device (or at least a partialassembly) is provided pre-attached to a sample cartridge with thefluid-tight couplings coupled with corresponding fluid ports of thecartridge. For example, a sample cartridge may be provided alreadycoupled with the fluid sample adapter 201 such that an end-user caninsert any chip within a chip carrier 230 component and couple withinthe flowcell portion 220 to facilitate sample detection with a chip.

C. Flowcell Portion

The flowcell portion of fluid sample adapter 201 is configured with anopen chamber that, when interfaced with an active area of a chip withinthe chip carrier, forms an enclosed flowcell chamber to facilitateanalysis of the fluid sample with the chip. The flowcell is shaped andconfigured to fluidly couple with a chip within a chip carrier attachedto the fluid sample adapter 201. Typically, the fluidic pathway of thefluid flow portion fluidically connects to the flowcell chamber throughfluid ports 226, 228 located at the top and bottom of the flowcellchamber. The chamber is formed by raised lands or ridges that come incontact with the active silicon or glass element used in the detectionscheme. The active element is located on the chip carried within thechip carrier and secured to the flowcell by bonding and sealing, whichcan be accompished by various means (e.g. using epoxy preforms,dispensed epoxy or other adhesives, a gasket, a gasket with adhesive,mechanical features, or various other means). The purpose of theflowcell adapter is to create a complete flowcell chamber, bounded bythe detection surface on one side and the flowcell adpater on theremaining sides. The flowcell portion 220 also includes one or morecoupling features 229 defined as alignment and assembly bosses as wellas mechanical snaps that are received in corresponding holes 239 of achip carrier 230 to align and securely couple the chip carrier 230 withthe flowcell portion 220, as shown in the cross-sectional view A-A inFIG. 4C.

FIG. 4B illustrates detailed views of an example flowcell portion 220for use with the chip device 200. In this embodiment, the flowcelladapter 220 is configured to fluidly communicate with the fluid flowportion 210 shown in FIG. 4A. As shown in FIG. 4B, flowcell portion canbe formed within a planar substrate formed of a rigid material (e.g.polymer or any suitable material) so as to define the open flowcellchamber 224, and flowcell ports 226, 228. Flowcell portion 220 isfurther configured to couple with the chip carrier so as to form anenclosed flowcell chamber with the active area of the chip carriedwithin. The top and bottom flowcell ports 226, 228 fluidly couple theflowcell chamber with fluid channels of the fluid flow portion to allowcontrolled flow of fluid sample into or out of the flowcell chamber uponcontrolled pressurization of the inlet and outlet 212, 214 of the chipcarrier device 200 fluidly coupled with the sample cartridge 100.

D. Chip Carrier

FIGS. 5A-5C illustrate detailed views of a chip carrier 230 of the chipcarrier device, in accordance with some embodiments. As can be seen inFIG. 5A, chip carrier 230 is defined within a substantially planarsubstrate 231 that includes a contoured region 236 dimensioned toreceive the chip and configured with multiple electrical contacts 234arranged to electrically connect with corresponding contacts of the chipwhen received within. In this embodiment, the contoured region 236 issquare and electrical contacts 234 configured to receive and couple witha chip, such as shown in FIG. 5A. Contoured region 236 includes a raisedridge along the perimeter thereof to engage a corresponding portion ofthe flowcell portion and effectively seal the chip within the chipcarrier device. The raised lands or ridge around the open flowcellchamber engage an active surface of the chip so as to form an encloseflowcell chamber, as described above.

The electrical contacts 23 are electrically coupled with correspondingcontact array 232 of an electrical interface board disposed on anopposite side of the chip carrier 230, as shown in FIG. 5B. The contactarray 232 is defined as an array of enlarged contact pads arranged tofacilitate contact with corresponding electrical contacts, typicallypogo pins, of the instrument interface 300 of the module. FIG. 5C showsa cross sectional view of chip carrier 230 with a chip carried andelectrically coupled within receptacle 236. Wire bonds are not shown inthis view. The electrical interface board can also host passive andactive electronic components in addition to those of the chip carrier asneeded for various other tasks. For example, such components couldinclude any components needed for signal integrity, amplification,multiplexing or other such tasks.

E. Chip

In some embodiments, if the chip 240 includes a silicon sensor element,it can be bonded within the chip carrier 230 and wire bonds applied toconnect the silicon element electrically to the chip carrier 230. Inother embodiments, the chip can merely be pressed into the recess suchthat the friction fit provides sufficient electrical contact betweencorresponding contacts.

In some embodiments, the chip 240 is a semiconductor diagnostic chip. Insome embodiments, the semiconductor diagnostic chip is configured toperform sequencing of a nucleic acid target molecule by nanoporesequencing, which detects changes in electrical conductivity and doesnot require optical excitation or detection. The underlying technologiesof such chips can be further understood by referring to U.S. Pat. No.8,986,928. In some embodiments, the semiconductor diagnostic chipanalyzes other attributes of a target molecule in the sample, such asmolecular weight and similar characteristics. Such technologies can befurther understood by referring to: Xiaoyun Ding, et al. Surfaceacoustic wave microfluidics. Lab Chip. 2013 Sep. 21; 13(18): 3626-3649.In some embodiments, the semiconductor diagnostic chip uses surfaceplasmon resonance to provide analysis of a target molecule, for exampleas used in the Biocore™ systems provided by GE Healthcare UK Limited andas described in their Biocore Sensor System Handbook (seegelifesciences.com/biacore). The entire contents of each of the abovereferences are incorporated herein by reference in their entirety. Whilesemiconductor diagnostic chips are preferred, it is appreciated that theconcepts described herein are applicable to any type of chip suitablefor use in performing processing or analysis of a fluid sample.

It is appreciated that the chip carrier device can be configured for usewith any type of semiconductor chip, including but not limited to CMOS,ISFET, bulk acoustic, non-bulk acoustic chips, piezo-acoustic, and porearray sensor chips. Further, the chip can be adapted for use in an openpackage to any of the many JDEC standards, including but not limited toQFN, dual in-line, and BGA array. Alternatively, the chip can be mounteddirectly to the PCB as a chip-on-board assembly.

F. Assembly and Use of Chip Carrier Device

FIGS. 6A and 6B illustrate a perspective view and a cross-section viewof a chip carried within an assembled chip carrier device 200, along thesame sectional view as shown in the individual component section views.Each of the components of the chip carrier device, the fluid flowportion 210 and flowcell portion 220 of the fluid sample adapter 201 andthe chip carrier 230, can be seen interfaced via one or more couplingfeatures such that the fluid channels of the fluid flow portion 210fluidically coupled with the flowcell portion 220 to facilitateprocessing or analysis of the fluid sample with the semiconductor chipcarried within the chip carrier adjacent the flowcell. The electricalcontacts 232 of the chip carrier 230 face outward for engagement withcorresponding contacts of the instrument interface 300 to facilitatecontrol of the semiconductor chip with the module, as described above.

FIGS. 7A-7B illustrates detail views of the assembled chip carrierdevice 200 before coupling with the sample cartridge 100. While thesecomponents of the chip carrier device 200 are coupled and aligned byremovable coupling features 229, it is appreciated that such componentscould be coupled with non-removable coupling feature or permanentlybonded, such as by an adhesive or heat sealing. It is furtherappreciated that the components could be defined to receive the chip invarious other ways, for example, the components could be hinged orpartly attached along one side. Alternatively, the fluid sample adapterand chip carrier component could be formed as one integral component.

FIG. 8 illustrates a detail view of the sample cartridge 100 coupledwith a fluid sample adapter 201 via the fluidic interface 211 (the othercomponents of the chip carrier device have been omitted for improvedvisibility). FIG. 9 shows the assembled chip carrier device 200 coupledto the sample cartridge 100 via the fluidic interface 211 of the fluidicsample adapter 201. An end-user can assemble the chip carrier device andcouple with the sample cartridge in this fashion, before placing thesample cartridge containing a fluid sample within the module forprocessing and analysis with the chip carried within the chip carrierdevice 200.

III. Alternative Example Chip Devices and Associated Systems A. SystemOverview

FIG. 10 illustrates a detail view of the sample cartridge 1100fluidically coupled with chip carrier device 1200, in accordance withsome embodiments. In this embodiment, the chip carrier device 1200includes a fluid sample adapter 1210, flowcell adapter 1220 and a chipcarrier 1230. The fluid sample adapter 1210 fluidically couples to thesample cartridge 1100 by a pair of fluid ports on the sample cartridge;the flowcell adapter 1220 is fluidically coupled to the fluid sampleadapter 1210; and the chip carrier 1230 is coupled to the flowcelladapter 220 such that a chip carried in the chip carrier 1230 along withthe flowcell adapter 1220 defines the flowcell. Any or all of theadapters or chip carrier of the chip carrier device 1200 are formed froma suitably rigid material such that the carrier device 1200 extendsoutward from the sample cartridge 1100. In some embodiments, the chipcarrier device 200 is supported only by a pair of inlet stubs of thefluid sample tube adapter 1210 fittingly received within thecorresponding pair of fluid ports of sample cartridge 1100 and asurrounding flange.

B. Fluid Sample Adapter

FIGS. 10-17 depicts exemplary chip carrier device assemblies andcomponents in accordance with some embodiments. Such device assembliescan include a fluid sample adapter, a flowcell adapter and chip carriercomponent. As shown in FIG. 11A, the fluid sample adapter 1210 includestwo fluid channels or conduits spaced apart and extending within thechip carrier device. The channels are separated and supported by asupporting web structure. The chip carrier device can be fabricated fromany material suitable for transport of a fluid sample selected so as tonot interfere with processing or analysis of the sample, typically aninert plastic or polymer-based material can be used. In someembodiments, the components of the chip carrier device are formed ofpolycarbonate, polysulfone, or any suitable material (e.g. any materialcompatible with an adhesive). In some embodiments, the material can becompatable with a silicone adhesive. In some embodiments, the materialused to fabricate the chip carrier device is a transparent or partlytranslucent material to allow visual observation of sample transportand/or optical detection/monitoring of the fluidic channel through thematerial.

In some embodiments, the chip carrier device includes a fluid sampleadapter configured with the same Luer ports and flange arrangement ofthe fluidic interface as a typical PCR reaction tube so that the fluidsample adapter can easily interface with sample cartridges. The fluidsample adapter is configured such that the ports connect fluidically toan optional PCR pre-amplification chamber. Alternatively, theamplification chamber could house a filter, an affinity matrix, amagnetic capture zone, or other active area that can be manipulated bythe module. Typically, the fluidic pathways are defined in a firstsubstrate and sealed by a second substrate, such as a thin film, similarto the construction of conventional PCR reaction tubes. In someembodiments, the fluid sample adapter also features alignment andassembly bosses as well as mechanical snaps so that a flowcell adaptercan be positioned and secured to the reaction tube adapter with ease.

In some embodiments, the length of the fluid sample adapter is about 12cm, 11 cm, 10 cm, 9 cm, 8 cm, 7 cm, 6 cm, 5 cm, 4 cm, 3 cm, 2 cm, or 1cm in length. In some embodiments, the fluid sample adapter 210 has alength between 3 to 5 cm, such as about 4 cm from the flange of thefluidic interface 211, and the fluid channels extend in parallel and areseparated by about 1 cm. This configuration allows for substantiallyfluid-tight couplings that are of substantially the same construction asa conventional reaction tube. The fluid-tight couplings of each channelare defined by a stub, each stub being dimensioned to be fittinglyreceived in a corresponding external port of the sample cartridge tofacilitate a fluid-tight coupling of the fluid channels withcorresponding fluid channels of the chip carrier device. For example,stubs along fluid inlets and outlet 1212, 1214 at the proximal end ofthe chip carrier device 1200 serve as inlet stubs for flow of theprepared fluid sample into the chip carrier device 1200, while stubs ofthe flowcell ports 1216′, 1218′ form fluid-tight couplings to facilitateflow of the prepared fluid sample into the flowcell chamber of theflowcell adapter. In some embodiments, these stubs can have an outsidediameter between 2-10 mm, for example, the outside diameter can be 2, 3,4, 5, 6, 7, 8, 9, or 10 mm. Typically, the outside diameter of the stubis about 3 mm, and extends from the flange a distance of about 2-5 mm,such as about 3 mm, to facilitate fluid-tight coupling. In someembodiments, the inside diameter of each of the one or more channelswithin any of the components of the chip carrier device can be within arange of 1 mm to 5 mm.

In some embodiments, the fluid sample adapter 1210 includes one or morechannels that extend between fluid-tight couplings without any chambers,valves or ports between the proximal and distal ends. In someembodiments, the fluid sample adapter 1210 includes one or more valves,or ports. In some embodiments, the one or more channels can include oneor more chambers or regions, which can be used to process or analyze thefluidic sample. For example, the fluid sample adapter can include one ormore chambers or regions for thermal amplification of a nucleic acidtarget in the sample, filtration of the sample, chromatographicseparation of the sample, hybridization, and/or incubation of the samplewith one or more assay reagents.

While the fluid tight couplings shown in FIG. 11A includes stubsextending from a flange of the fluidic interface 1210, it is appreciatedthat various other fluid-tight couplings suitable for use with theinvention can be devised as needed to fluidly couple with other types ofdevices. Non-limiting exemplary fluid type couplings suitable for usewith the invention, include, Luer-lock connections, snap-fitconnections, friction fittings, click-fit connections, and screw-onconnections. Additional types of fluid tight couplings suitable for usewith the invention are well known to persons of skill in the art.

As can be seen in FIGS. 11A-11B, the fluid sample adapter 1210 isdefined by one or more planar substrates defining a fluidic path 1213coupled to a fluidic interface 1211. The fluidic interface 1211 is astructural member which a majority of the planar frame cantilevers. Thefluidic interface 1211 can be integrally formed with the planar frame.The fluidic interface 1211 also serves as a mechanical coupling tosample cartridge 100. Fluidic interface 1211 includes a fluidic inlet1212 and fluidic outlet 1214, which provides a fluidic interface to thesample cartridge device. Each of the fluidic inlet 1212 and fluidicoutlet 1214 are fluidically coupled to fluidic path 1213 that is formedin the planar substrate.

In some embodiments, the fluidic path 1213 is defined primarily alongone major face of the planar substrate and enclose by a second planarsubstrate, for example, a thin film heat sealed on the substrate so asto enclose the channels and chambers defined within the substrate. Thefluidic path 1213 leads to a flowcell interface that includes a firstset of flowcell ports 1216, 1218 extending laterally or traverse to theplane of the adapter, typically perpendicular, so as to fluidicallycouple with a fluidic path of a flowcell adapter (see FIGS. 12A-5C)coupled to the fluid sample adapter 1210 along a major face thereof. Inthis embodiment, the flowcell interface includes an inlet flowcell port1216 and outlet flowcell port 1218, which allow for controlled fluidtransport through the chip carrier device 1200 into the flowcell chambervia the fluidic inlet 1212 and fluidic outlet 1214. In this embodiment,the fluidic channels are defined along one major face of the fluidsample adapter 1210 and the flowcell adapter is coupled to an opposingmajor face. In such embodiments, the first set of ports 1216 and 1218are defined in the same major face in which the channels are formed, asshown in FIG. 11B. Flowcell ports 1216, 1218 lead to correspondingchannels that extend transversely through the adapter and open along anopposing major face within corresponding protruding stubs 1216′, 1218′,as seen in the sectional view in FIGS. 11B and 11C. These protrudingstubs facilitate fluid-tight coupling with corresponding fluid ports inthe flowcell adapter when coupled thereto. While shown as separatecomponents here, it is appreciated that components of the chip carrierdevice can be formed as integral components. For example, the componentsdepicted in FIGS. 11A-12A can be formed as portions of an integralcomponent.

It should be understood that use of the terms “inlet” and “outlet” donot limit function of any fluid inlets or outlets described herein.Fluid can be introduced and evacuated from both or either. In someembodiments, the fluidic path 1213 is valveless, and thus externalincreases or decreases in pressures can be applied via the fluidic inlet1212 and fluidic outlet 1214 by an external system to move fluid withinthe fluidic path 1213, which extends from the fluidic inlet 1212 to thefluidic outlet 1214. The cross-section of the fluidic path 1213 can beround or rectangular, and can have diameters or widths ranging fromabout 50 μm to about 2 mm. Typically, the diameters or widths range fromabout 250 μm to about 1 mm. In this embodiment, the fluidic path 1213includes a chamber 1215, which is an enlarged portion of fluidic path1213 dimensioned to contain a substantial portion or an entirety of afluid sample transported from the sample cartridge to facilitate variousprocesses, including but not limited to flow metering, mixing,pre-amplification, thermal cycling, or any other sample processingdesired. It is appreciated that various other components could beincorporated into fluid sample adapter, for example, a valve, filter,window, or any other feature desired.

The fluid sample adapter 1210 further includes one or more couplingand/or alignment features. In this embodiment, the fluid sample adapterincludes coupling feature 1219, which here is defined as a notchedregion that is shaped to receive and a corresponding feature along adistal outside edge of the flowcell adapter so as to couple the flowcelladapter thereto. The coupling feature 1219 can be defined so as toresiliently deflect to receive the flowcell adapter and secure theflowcell adapter when fitted within the recessed notched portion. Inthis embodiment, the fluid sample adapter further includes alignmentfeature 1219′ that fits into a corresponding alignment feature on theflowcell adapter, which facilitate proper alignment and orientation ofthe flowcell adapter when coupled thereto to ensure a fluid-tightcoupling between the first set of flowcell ports and corresponding fluidports of the flowcell adapter. In this embodiment, the alignment feature119′ is defined as a circular protrusion with a central hole. It isappreciated that various other coupling features and alignment featurescould be used (e.g. interfacing contoured regions, snap-fit feature,etc.) and that such features could be separate features or integratedinto a single feature. In some embodiments the fluid sample adapter andflowcell adapter could be fixedly secured together by heat sealing,adhesive or any suitable means. In still other embodiments, the fluidsample adapter and flowcell adapter could be integrally formed as asingle component.

In some embodiments, the chip carrier device (or at least a partialassembly) is provided pre-attached to a sample cartridge with thefluid-tight couplings coupled with corresponding fluid ports of thecartridge. For example, a sample cartridge may be provided alreadycoupled with the fluid sample adapter 1210 and attached to flowcelladapter such that an end-user can insert any chip within a chip carrier1230 component and then couple within the chip carrier to the flowcelladapter 1220.

C. Flowcell Adapter

In some embodiments, the chip carrier device includes a flowcell adapterconfigured with an open chamber that when interfaced with an active areaof a chip within the chip carrier, forms an enclosed flowcell chamber tofacilitate analysis of the fluid sample with the chip. In someembodiments, the flowcell is configured to fluidly couple with the fluidsample adapter and the chip within the chip carrier. Typically, theflowcell adapter connects to the flowcell chamber through fluid portslocated at the top and bottom of the chamber. The chamber is formed byraised lands or ridges that come in contact with the active silicon orglass element used in the detection scheme. The active element islocated on the chip carried within the chip carrier and secured to theflowcell by bonding and sealing, which can be accompished by variousmeans (e.g. using epoxy preforms, dispensed epoxy or other adhesives, agasket, a gasket with adhesive, mechanical features, or various othermeans). The purpose of the flowcell adapter is to create a completeflowcell chamber, bounded by the detection surface on one side and theflowcell adpater on the remaining sides. The flowcell adapter alsofeatures alignment and assembly bosses as well as mechanical snaps sothat the flowcell adapter can be positioned and secured to the fluidsample adapter with ease.

FIGS. 12A-12C illustrate detailed views of an example flowcell adapter1220 for use with the chip carrier device 1200. In this embodiment, theflowcell adapter 1220 is configured to fluidly couple with the fluidsample adapter 1210 shown in FIG. 11A. As shown in FIG. 12A, flowcelladapter 1220 is a planar substrate 1221 formed of a rigid material (e.g.polymer or any suitable material) having a recessed portion 1222, anopen flowcell chamber 1224, channel 1225, and flowcell ports 1226, 1228defined therein. Flowcell adapter 1220 is configured to couple with thefluid sample adapter 1210 along one major face and with a chip with thechip carrier along an opposing major face thereof. The open chamber 1224forms an enclosed flowcell chamber with the active area of the chip whenthe chip is engaged within the correspondingly shaped recess 1224. Thetop and bottom flowcell ports 1226, 1228 fluidly couple the flowcellchamber with the set of flowcell ports of the fluid sample adapter 1210so as to allow flow of fluid sample into or out of the flowcell chamberupon controlled pressurization of the inlet and outlet 1212, 1214 of thechip carrier device 1200 fluidly coupled with the sample cartridge 1100.Channel 1225 extends into the flowcell chamber and allows for any of:access into the flowcell chamber, injection of materials into theflowcell chamber, capture of any bubbles within the flowcell chamber,and pressure regulation.

As can be seen in FIG. 12B and the sectional view in FIG. 12C, each offluid ports 1226 and 1228 extend to the opposing major face of flowcelladapter 1220 and open within a recessed hole or chamber of a boss 1226′,1228′ so as to form a fluid-tight coupling with the ports within thecorresponding cylindrical protrusions or stubs of the fluid sampleadapter. It is appreciated that various other fluid-tight couplingscould be used to fluidically couple the flowcell adapter 1220 to thefluid sample adapter 1210.

Flowcell adapter 1220 further includes one or more coupling and/oralignment features. In this embodiment, the flowcell adapter includes acoupling feature 1229, which here is defined as a tab region that isshaped to be resiliently received within a corresponding notched region1219 of the fluid sample adapter 1210. Flowcell adapter includes raisedridges 1229′ along each side edge that engage corresponding features(e.g. groove, ridge, etc.) of the fluid sample adapter to further assistin alignment and coupling of the adapters. In this embodiment, theflowcell adapter further includes alignment features 1229 a that fitinto corresponding features on the fluid sample adapter to ensure properalignment and orientation of the flowcell adapter when coupled theretoso as to ensure fluid-tight coupling between the first set of ports andcorresponding fluid ports of the flowcell adapter. In this embodiment,the alignment features 1229 a are each defined as a circular protrusionthat fit into corresponding alignment holes 1219 a of fluid sampleadapter 1210. It is appreciated that various other coupling features andalignment features could be used (e.g. interfacing contoured regions,snap-fit feature) and that such features could be separate or integratedinto a single feature. In some embodiments, the fluid sample adapter andflowcell adapter could be fixedly secured together by heat sealing,adhesive or any suitable means. In some embodiments, the fluid sampleadapter and flowcell adapter could be integrated into a singlecomponent.

D. Chip Carrier

FIGS. 13A-13C illustrate detailed views of a chip carrier 1230 of thechip carrier device, in accordance with some embodiments. As can be seenin FIG. 13A, chip carrier 1230 is defined within a substantially planarsubstrate 1231 that includes a contoured region 1236 dimensioned toreceive the chip and configured with multiple electrical contacts 1234arranged to electrically connect with corresponding contacts of the chipwhen received within. In this embodiment, the contoured region 1236 issquare and electrical contacts 1234 configured to receive and couplewith a chip, such as shown in FIG. 13A. Contoured region 1236 includes araised ridge along the perimeter thereof to engage a correspondingportion of the flowcell adapter and effectively seal the chip within thechip carrier device. The raised lands or ridge around the open flowcellchamber engage an active surface of the chip so as to form an encloseflowcell chamber, as described above.

The electrical contacts 123 are electrically coupled with correspondingcontact array 1232 of an electrical interface board disposed on anopposite side of the chip carrier 1230, as shown in FIG. 13B. Thecontact array 1232 is defined as an array of enlarged contact padsarranged to facilitate contact with corresponding electrical contacts,typically pogo pins, of the instrument interface 1300 of the module.FIG. 13C shows a cross sectional view of chip carrier 1230 with a chipcarried and electrically coupled within receptacle 1236. Wire bonds arenot shown in this view. The electrical interface board can also hostpassive and active electronic components in addition to those of thechip carrier as needed for various other tasks. For example, suchcomponents could include any components needed for signal integrity,amplification, multiplexing or other such tasks.

E. Chip

In some embodiments, if the chip 1240 includes a silicon sensor element,it can be bonded within the chip carrier 1230 and wire bonds applied toconnect the silicon element electrically to the chip carrier 1230. Inother embodiments, the chip can merely be pressed into the recess suchthat the friction fit provides sufficient electrical contact betweencorresponding contacts.

In some embodiments, the chip 1240 is a semiconductor diagnostic chip,such as any of those described herein. While semiconductor diagnosticchips are preferred, it is appreciated that the concepts describedherein are applicable to any type of chip suitable for use in performingprocessing or analysis of a fluid sample.

It is appreciated that the chip carrier device can be configured for usewith any type of chip, including but not limited to CMOS, ISFET, bulkacoustic, non-bulk acoustic chips, piezo-acoustic, and pore array sensorchips. Further, the chip can be adapted for use in an open package toany of the many JDEC standards, including but not limited to QFN, dualin-line, and BGA array. Alternatively, the chip can be mounted directlyto the PCB as a chip-on-board assembly.

F. Assembly and Use of Chip Carrier Device

FIGS. 14A and 14B illustrate sectional views of the assembled chipcarrier device 200, along the same sectional view as shown in theindividual component section views. Each of the components of the chipdevice, the fluid sample adapter 1210, the flowcell adapter 1220 and thechip carrier 1230, can be seen interfaced via one or more couplingfeatures such that the fluid channels of the fluid sample adapter 1210are aligned and fluidically coupled with the flowcell of the flowcelladapter 1220 to facilitate processing or analysis of the fluid samplewith the semiconductor chip carried within the chip carrier adjacent theflowcell. The electrical contacts 1232 of the chip carrier 1230 faceoutward for engagement with corresponding contacts of the instrumentinterface 1300 to facilitate control of the semiconductor chip with themodule, as described above.

FIGS. 14A and 14B illustrate a detail view of the chip carrier interface1230 fluidically coupled with the flowcell adapter 1220. FIGS. 15A and15B illustrate detail views of the fully assembled chip carrier device200, before fluidically coupling with the sample cartridge 100 and FIG.15C illustrates a cross-sectional view of the device. As shown, thedevice is configured such that a semiconductor chip 1240 within thecarrier 1230 is exposed to the flowcell of the flowcell adapter 1220.While these components are coupled and aligned with removable couplingfeatures to allow an end-user to assemble any chip within the device, itis appreciated that such components could be coupled with non-removablecoupling feature or permanently bonded, such as by an adhesive or heatsealing. It is further appreciated that the components could be definedto receive the chip in various other ways, for example, the componentscould be hinged or partly attached along one side. FIGS. 15A and 15Billustrate detail views of the chip carrier device 200, beforefluidically coupling with the sample cartridge 100 and FIG. 15Cillustrates a cross-.

FIG. 16 illustrates a detail view of the sample cartridge coupled with afluid sample adapter 1210 fluidically attached to the sample cartridge1100 via the fluidic interface 1211 (the other components of the chipcarrier device have been omitted for improved visibility). FIG. 17 showsthe fluid sample adapter 1210 coupled with the flowcell adapter 1220 andthe chip carrier 1230 within the overall chip carrier device 1200, achip (not shown) carried within the chip carrier 1230. An end-user canassemble the chip carrier device and couple with the sample cartridge inthis fashion, before placing the sample cartridge containing a fluidsample within the module for processing and analysis. FIGS. 18A and 18Billustrate detail views of the chip carrier device 200, beforefluidically coupling with the sample cartridge 100.

FIG. 18 illustrates alternative detection modes configured for use witha sample cartridge, in accordance with some embodiments. Embodiment 0depicts a sample cartridge 100 fluidically coupled with a reaction tube110. Embodiment 1 depicts a sample cartridge 100 fluidically coupledwith a fluidic bridge 120 adapted to facilitate transport of the fluidsample to an external device for further processing or analysis.Embodiment 2 depicts a sample cartridge 100 fluidically coupled with achip carrier device 200 carrying a semiconductor detection chip, asdescribed herein. Embodiment 3 depicts an alternative construction of achip carrier device 200′ carrying a semiconductor detection chip inaccordance with the concepts described herein. In this embodiment,certain components of the chip carrier device have been eliminated byutilizing either a chip-on-board and epoxy preform structure or verticalinterconnect access such as a bare through-silicon-via (“TSV”), or glassintegrated into a molded carrier tube. This design reduces the number ofcomponents, thereby reducing the complexity and cost of the chip carrierdevice to allow for high volume production methods. Further, this designconcept allows for a plug-n-play approach, allowing the system to beused a platform to readily accept and utilize existing “lab on a chip”devices in a more cost effective manner. While in these embodiments, thechip carrier devices are configured to carry the detection chip in avertical orientation, it is appreciated that various otherconfigurations and orientations could be utilized. In some embodiments,utilizing a chip carrier device that orients the detection chipvertically is advantageous as it further reduces the size of the overallchip carrier device so as to fit within a conventional sample processingmodule modified with an instrument interface for controlling analysiswith the chip.

IV. Methods of Sample Processing Utilizing Chip Carrier Device

FIGS. 19-20 illustrates exemplary methods of processing a fluid samplewith a semiconductor chip utilizing a chip carrier device and a samplecartridge, in accordance with some embodiments.

FIG. 19 depicts a method that includes steps of: receiving, within areceptacle of a sample processing module, a sample cartridge containinga fluid sample therein. Such a module can be the module described hereinor any such module or similar modules known in the art capable ofreceiving and processing a sample cartridge as described herein. Themethod further includes steps of: performing, with the module, one ormore sample processing steps on the fluid sample within the samplecartridge and transporting the processed fluid sample from the cartridgeinto a chip carrier device fluidly coupled with the sample cartridge.Transporting of the processed fluid sample can be performed throughcontrolled pressurization through fluid ports of the sample cartridgethrough which the carrier device is attached. The method furtherincludes performing, with the module, analysis of the processed fluidsample with a semiconductor chip carried within the chip carrier device.In some embodiments, a diagnostic result of the fluid sample analyzedwith the chip is received by the module or determined by the modulethrough the instrument interface.

FIG. 20 depicts a method that includes steps of: providing a chipcarrier device having a fluid sample adapter, a flowcell and a chipcarrier carrying a semiconductor chip. Such components could be asdescribed above or could include various modification or additionaladapters as would be understood by one of skill in the art. The methodscan further include: fluidly coupling the chip carrier device to asample cartridge containing a fluid sample and placing the cartridgeinto a processing module and receiving a processed fluid sample from asample cartridge within a fluid sample adapter of a chip carrier devicevia one or more fluid ports of the fluid sample adapter. The methods canfurther include transporting the processed fluid sample from the fluidsample adapter into a flowcell of the chip carrier device via a firstset of flowcell ports. In some embodiments, the chip carrier device isvalveless such that receiving and transporting the fluid sample therethrough is performed by controlled pressurization of one or more fluidports of the sample cartridge through which the chip carrier device isfluidically coupled. The methods can further include: performinganalysis of the processed fluid sample within the flowcell with adiagnostic semiconductor chip carried within a chip carrier of the chipcarrier device.

As noted previously, in one aspect, the adapter allows for interfacingwith a chip that is not within a conventional chip package (e.g. a chipmounted within a leaderframe wire bonded, potted in epoxy), therebyproviding improved ease of use and assembly, further reduced size andintegration as compared to conventional approaches. In some embodiments,the chip carrier device can include a set of standard open chip carriersinto which the chip may be packaged. In other embodiments, the devicecan include a chip-on-board packaging that allows the chip to beinserted and interfaced with a flowcell, as described above.

In the foregoing specification, the invention is described withreference to specific embodiments thereof, but those skilled in the artwill recognize that the invention is not limited thereto. Variousfeatures, embodiments and aspects of the above-described invention canbe used individually or jointly. Further, the invention can be utilizedin any number of environments and applications beyond those describedherein without departing from the broader spirit and scope of thespecification. The specification and drawings are, accordingly, to beregarded as illustrative rather than restrictive. It will be recognizedthat the terms “comprising,” “including,” and “having,” as used herein,are specifically intended to be read as open-ended terms of art.

1-42. (canceled)
 43. A chip carrier comprising: a planar framecoupleable with a flowcell portion of a fluid adapter; an open carrierportion configured to receive and support a chip; and an electricalinterface having a plurality of electrical contacts electricallyconnected to the open carrier portion so as to electrically couple withelectrical contacts of the chip when carried within the carrier portion.44. The chip carrier of claim 43, wherein the open carrier portion isconfigured for receiving a chip.
 45. The chip carrier of claim 43,wherein the open carrier portion is configured to support the chip in avertical orientation.
 46. The chip carrier of claim 43, wherein the opencarrier portion is configured for receiving any of the following typesof chips: CMOS, ISFET, bulk acoustic, non-bulk acoustic, piezo-acousticand pore array sensor chips.
 47. The chip carrier of claim 43, furthercomprising: a coupling and/or alignment feature to securely couple thefirst major side of the planar frame to a planar surface of a flowcelladapter at least partly defining a flowcell chamber defined therein suchthat when the chip carrier carries an active element and is coupled tothe flowcell adapter, the flowcell chamber is defined between theflowcell adapter and the active element.
 48. The chip carrier of claim43, wherein the open carrier portion is disposed on a first major sideof the planar frame.
 49. The chip carrier of claim 48, wherein theplurality of electrical contacts are disposed along a second major sideof the planar frame opposing the first major side.
 50. The chip carrierof claim 48, wherein the plurality of electrical contacts are arrangedso as to interface with corresponding contacts of a chip control boardof a module when the chip carrier is coupled within a chip carrierdevice and fluidically coupled with a sample processing cartridgeoperably coupled within the module.
 51. The chip carrier of claim 43,wherein the electrical interface includes one or more active componentsconfigured for signal integrity, amplification, multiplexing or anycombination thereof.
 52. A module for performing sample processing, themodule comprising: a cartridge receiver adapted to receive and removablycouple with a sample cartridge configured to hold an unprepared sample,the sample cartridge comprising a plurality of processing chambersfluidically interconnected by one or more mechanisms, wherein thecartridge receiver includes: a cartridge interface unit configured formoving the valve body to change fluidic interconnections between theplurality of sample processing chambers, a pressure interface unit forapplying pressure to move fluid among the plurality of processingchambers according to position of the valve body, and a samplepreparation controller configured to electronically communicate with theassay processing device and configured to control the cartridgeinterface unit and pressure interface unit to process the unpreparedsample into a prepared sample within the sample cartridge; and a chipcontrol unit component having an instrument interface with a pluralityof contacts arranged to interface with contacts of an electricalinterface of a chip carrier device fluidly coupled with the samplecartridge when received within the cartridge receiver to facilitateanalysis of the sample using a chip carried within the chip carrierdevice.
 53. The module of claim 52, wherein the chip control unitincludes one or more active components configured for signal integrity,amplification, multiplexing or any combination thereof.
 54. The moduleof claim 52, wherein the module further comprises: a processor unitconfigured to perform an analysis of a fluid sample exposed to an activeelement of the chip supported in the chip carrier device via theplurality of contacts of the instrument interface.
 55. A method forprocessing a sample, the method comprising: receiving a sample cartridgeat a cartridge receiver of a module, the sample cartridge comprising aplurality of processing chambers fluidically interconnected by a one ormore mechanisms; receiving an electronic instruction to process theunprepared sample into a prepared sample from a processing control unitof the cartridge receiver; performing a sample preparation method toprocess the unprepared sample into the prepared sample; fluidicallymoving the prepared sample into a chip carrier device fluidly coupledwith the sample cartridge; and performing an analysis of the fluidsample using an active element of a chip supported within the chipcarrier device via processing control unit of the cartridge receiverelectrically coupled with the chip.
 56. The method of claim 55, whereinperforming the sample preparation comprises moving a cartridge interfaceunit to move a valve body of the sample cartridge to change fluidicinterconnections between the plurality of sample processing chambers ofthe sample cartridge; and applying pressure to a pressure interface unitto move fluid between the plurality of processing chambers according toa position of the valve body.
 57. The method of claim 55, whereinanalysis of the fluid sample is performed within a flow cell of the chipcarrier device and is controlled by the processing unit via a pluralityof contacts of an electrical interface of the chip carrier device. 58.The method of claim 55, further comprising: coupling a no-leads chiphaving the active element within a carrier portion of the chip carrierdevice, wherein the no-leads chips is configured to perform analysis ofa fluid sample with the active element.
 59. The method of claim 58,wherein coupling the no-leads chip within the chip carrier devicecomprises: coupling the chip within a chip carrier adapter having thecarrier portion and an electrical interface with a plurality ofelectrical contacts; coupling the chip carrier with a flowcell adapterdefining a flowcell chamber between the flowcell adapter and the activeelement of the chip when coupled thereto; and coupling the flowcelladapter to a fluid sample adapter, the fluid sample adapter having afluidic interface configured to fluidically couple with the sampleprocessing cartridge so as to facilitate flow of the fluid sampletherein for analysis using the active element of the chip within thechip carrier device.